Optimization of parameters for semiempirical methods VI: more modifications to the NDDO approximations and re-optimization of parameters

Abstract

Modern semiempirical methods are of sufficient accuracy when used in the modeling of molecules of the same type as used as reference data in the parameterization. Outside that subset, however, there is an abundance of evidence that these methods are of very limited utility. In an attempt to expand the range of applicability, a new method called PM7 has been developed. PM7 was parameterized using experimental and high-level ab initio reference data, augmented by a new type of reference data intended to better define the structure of parameter space. The resulting method was tested by modeling crystal structures and heats of formation of solids. Two changes were made to the set of approximations: a modification was made to improve the description of noncovalent interactions, and two minor errors in the NDDO formalism were rectified. Average unsigned errors (AUEs) in geometry and ΔHf for PM7 were reduced relative to PM6; for simple gas-phase organic systems, the AUE in bond lengths decreased by about 5 % and the AUE in ΔHf decreased by about 10 %; for organic solids, the AUE in ΔHf dropped by 60 % and the reduction was 33.3 % for geometries. A two-step process (PM7-TS) for calculating the heights of activation barriers has been developed. Using PM7-TS, the AUE in the barrier heights for simple organic reactions was decreased from values of 12.6 kcal/mol-1 in PM6 and 10.8 kcal/mol-1 in PM7 to 3.8 kcal/mol-1. The origins of the errors in NDDO methods have been examined, and were found to be attributable to inadequate and inaccurate reference data. This conclusion provides insight into how these methods can be improved.Electronic supplementary materialThe online version of this article (doi:10.1007/s00894-012-1667-x) contains supplementary material, which is available to authorized users.

Two-dimensional covalent triazine framework as an ultrathin-film nanoporous membrane for desalination

“…In this case, we improve the salt rejection of the CTF--1 membrane by considering two different functionalized derivatives of the CTF--1 building block, CTF--1--Cl and CTF--1--CH 3 (see Figure 1 for their atomic structures, both CTF--1--Cl and CTF--1--CH 3 structures adopted in this work were relaxed using the semi--empirical PM7 method. 29 ). Figure 1(c) and 1(d) clearly indicates that the pore size of both CTF--1--Cl and CTF--1--CH 3 has been effectively reduced (see Table 1) compared to CTF--1.…”

Complex Chemical Reaction Networks from Heuristics-Aided Quantum Chemistry

“…[48][49][50] The energies are determined throughout this work by structure optimizations using the PM7 semiempirical method within the MOPAC package. 51 Solvation effects in water are included using the conductor-like solvation model (COSMO) 52 with an effective dielectric constant of ε = 78.4. We consider reactions involving one molecule glycolaldehyde and one formaldehyde molecule (F 1 ={O − − CHCH 2 OH, CH 2 − − O}, Fig.…”

Crystal structure, Hirshfeld analysis and molecular docking with the vascular endothelial growth factor receptor-2 of (3Z)-5-fluoro-3-(hydroxyimino)indolin-2-one

“…Initially, the semi-empirical equilibrium energy of the small molecule was obtained using the PM6 Hamiltonian, but the experimental bond lengths were conserved. The calculated parameters were: heat of formation = À49.353 kJ mol À1 , gradient normal = 0.90997, HOMO = À9.265 eV, LUMO = À1.337 eV and energy gap = 7.928 eV (Macrae et al, 2008;Stewart, 2013Stewart, , 2016. The biological target prediction for the title compound was calculated with the SwissTargetPrediction webserver based on the bioisosteric similarity to the isatin entity (Gfeller et al, 2013(Gfeller et al, , 2014.…”